mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Metagenomic Analysis of Human Decomposition
In a recent study published, in PLOS One, researchers from Baylor College of Medicine and Sam Houston State University, looked into the microbiome of human decomposition. The authors sought to identify microbial organisms that define the shift from early to late decomposition. This could aid forensic research by providing another and perhaps more unique marker for different stages of decomposition. Methodology The subjects used in the study were two caucasian males donated to the Southeast Texas Applied Forensic Science (STAFS) facility. The two subjects were aged 68 and 52 and died from acute myocardial infarction and carbon monoxide poisoning respectively. Their bodies were buried naturally in slightly acidic soil 5 km north of Huntsville, Texas where the climate is described as humid and subtropical and sparsely covered with pine trees and herbaceous plants. Both bodies were characterized as being in early decomposition stages when buried. One of the cadavers, STAFS 2011-006, was sampled from the 8th through the 15th of September 2011, and the second, STAFS 2011-016, was sampled from the 3rd through the 17th of November 2011. Daily temperature and humidity conditions were recorded. Bacterial samples were taken at placement and conclusion, described as early and late decomposition stages or pre- and post-bloat stages of decomposition. Early samples were taken from the mouth and rectum and late samples were taken from the mouth, small intestine, transverse and sigmoidal colon and stomach. A general body cavity swab was taken as well. Samples were amplified with the 16S rRNA gene and sequenced using 454 pyrosequencing. Bacterial DNA was isolated and the V3-V5 region of the 16S rRNA gene was amplified and sequenced. Following sequencing QIIME software was used for quality control and demultiplexing. Taxonomy was then defined using RDP Classifier. The samples were clustered into the following categories: Body site, sampling technique, decomposition stage and cadaver origin. Results The authors used a total body scoring system to determine the end stage of decomposition created by Megyesi et. al. '' Variable conditions and the fact that the total body scoring system is not perfect (since we do not know the exact temperature at which microbial activity ceases) the samples the authors were able to take from each cadaver varied. As discussed by the authors, many factors can alter the microbial species found during decomposition. These include the starting microbiome, the location of decomposition and the location of samples taken. Given this, the species richness increased as samples were taken from the upper intestinal tract to the lower intestinal tract. The authors then performed a cluster analysis to determine species diversity comparing the body sites. Pre-decomposition, oral and fecal samples showed highly divergent samples, each forming their own clusters and the whole body cavity sample showed mainly large intestinal bacteria. The most abundant phylum identified overall was Firmicutes followed by Proteobacteria. A large number of unclassified reads were also found in one of the two cadavers, particularly in small intestine samples while the second had relatively few unclassified reads. The Firmicutes phylum was dominant in fecal samples followed by Bacteroidetes in one body (STAFS-2011-016) but was dominated by Proteobacteria in the second body (STAFS-2011-006). Proteobacteria is not typically the dominant organism in a fecal sample, reflecting a potential pre-existing intestinal issue in one of the subjects. Looking more specifically into genera, lower G.I. tract and whole body organisms were relatively similar. ''Clostridium, Lactobacillus, Eggerthella, ''and ''Bacteroides ''were all identified. Oral genera differed in the two subjects, with one exhibiting many organisms consistent with a healthy human oral cavity and the other did not. The oral cavity was the only site that could be analyzed pre and post decomposition due to the integrity of the bodies. Depending on the sampling technique, one sample showed Proteobacteria and Firmicutes as the predominant phylum pre-decomposition and the other sample showed Firmicutes and Actinobacteria. Post-decomposition showed Firmicutes in one sample and Firmicutes and Proteobacteria in another. Overall the authors showed a shift from aerobic to anaerobic bacteria, with the predominant bacteria being ''Clostridia ''and ''Bacteroides during the process of decomposition. Lactobacillus and other Enterobacteriaceae were also identified but were not as abundant. Clostridia spp. are thought to be the primary species in lipid breakdown and Pseudomonas, ''Bacillus ''and other sulfate reducing bacteria are thought to be the primary species in protein breakdown. While ''Clostridia ''were found in abundance, ''Pseudomonas '' was only found pre-decomposition. However, as noted by the authors abundance does not equal metabolic significance and these bacteria could still be integral in breaking down protein. This study showed a relatively interesting approach to studying the microbiome of human body decomposition. In the future, it would be interesting to see a study where the authors had a better ability of sampling the body sites during decomposition since the current study was unable to test many of sites due to a lack in integrity. References 1. Hyde, E.R. ''et.al. ''The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. Plos One. 2013 Oct 30; 8(10):e77733. doi: 10.1371/journal.pone.0077733. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0077733#s2